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Winmostar tutorialGromacs

Solubility/χ/DPD parameterV7.021

X-Ability Co,. Ltd.

[email protected]

2017/07/06

mailto:[email protected]

I. MD of component 1 liquid phase

II. MD of component 1 gas phase

III. MD of component 2 liquid, gas phase

IV. Processing results

V. Parameters of DPD calculation

2017/07/06 Copyright (C) 2017 X-Ability Co.,Ltd. All rights reserved.

Contents

You must set up Cygwin to use Gromacs on Winmostar.

• Obtain the installer for Cygwin, which contains the all programs needed by

Winmostar, at https://winmostar.com/en/manual_en.html.

Configure


• When you change the installation path for Cygwin from the default one,

specify it on the preference panel.

https://winmostar.com/en/manual_en.html


• The simulation steps required are dependent on molecular species and

initial density.

• To obtain accurate and reproducible results, setting an extended

simulation time may be ideal.

• Methods for interaction calculations and/or force field also affect

simulation results.

Note

I. MD of component 1 liquid phase (modeling)


In this tutorial, component 1 is benzene.

1. Click -C6H5.

2. Click Repl to model a benzene.


1. Click File | Save as.

2. Save as benzene with file extension MOL2.

I. MD of component 1 liquid phase (modeling)


1. Click MD | Solvate/Build Cell.

2. Check Put the molecule on main window as solute.

3. Click Add mol2 File, and select benzene.mol2.

I. MD of component 1 liquid phase (build cell)


1. After opening the mol2 file, Set Enter # of molecules to 150, then Click OK.

2. Click Build.



The simulation cell will be displayed in the main window.



1. Click MD | Gromacs | Keywords Setup.

2. Click Reset.

3. Set Preset to Minimize (fast), # of Threads to a parallel number, then click OK.

I. MD of component 1 liquid phase (equalization 1)


1. Click MD | Gromacs | Start Gromacs.

2. Save the coordinate file as, c6h6_liquid.gro, the topology file as,

c6h6_liquid.top.

Cygwin will launch and Gromacs process will start.



1. After the calculation, click MD | Gromacs | Keywords Setup.

2. Check Extending Simulation. Set Preset to NVT (fast).

3. On Basic tab, set nsteps to 25000.

4. On Advance tab, set constraints to all-bonds, then click OK.





2. Set Preset to NPT (fast).

3. On Basic tab, set nsteps to 25000.

4. On Advance tab, set constraints to all-bonds, then click OK.




I. MD of component 1 liquid phase (product run)

Click MD | Gromacs | Start Gromacs to execute product run.

* No need to change keywords.


1. Click File | Open.

2. Open benzene.mol2.

II. MD of component 1 gas phase (build cell)



2. Click Reset.

3. Set Preset to Minimize (vapor, fast) , then click OK.


5. Save the coordinate file as c6h6_vapor.gro, topology file as c6h6_vapor.top.

II. MD of component 1 gas phase (equalization 1)


1. After the calculation, click MD | Gromacs | Keywords Setup.

2. Check Extending Simulation, then set Preset to NVT (vapor, fast).

3. On Advance tab, set constraints to all-bonds. Then click OK.


II. MD of component 1 gas phase (equalization 2)



2. On Basic tab, set gen-vel to no, then click OK.


II. MD of component 1 gas phase (product run)


• To get the solubility parameter of component 1, go to Ⅳ. Processing

results.

• For χ・DPD parameter, execute MD calculation of component 2 (liquid,

gas) described in the following pages.

III. MD of component 2


In this tutorial, component 2 is water.


2. Uncheck Put the molecule on main window as solute.

3. Click Add Water, then add 900 water molecules.

4. Set Set Density to 0.9, then click Build.

III. MD of component 2 liquid phase (Build cell)


The simulation cell will be displayed.

To calculate component 2 liquid phase, follow the MD calculation

(equilibration 1～3 and product run) of the component 1 liquid phase.

Save the coordinate file as h2o_liquid.gro, the topology file as

h2o_liquid.top.

III. MD of component 2 liquid phase (Build cell)



2. Uncheck Put the molecule on main window as solute.

3. Click Add Water, and add 1 water molecule.

4. Set Set Density to 0.001.

5. Click Build.

III. MD of component 2 gas phase (Build cell)


The simulation cell will be displayed.

(Please zoom out to display the molecule within the main window)

To calculate component 2 gas phase, follow the MD calculation (equilibration

1～3 and product run) of the component 1 gas phase.

Save the coordinate file as h2o_vapor.gro, the topology file as

h2o_vapor.top.

III. MD of component 2 gas phase


1. Click MD | Gromacs | Chi/DPD parameter.



On Molecule A tab, click Select... of each file,

1. On Liquid Phase, set edr File to gmx_tmp_mdrun.edr in c6h6_liquid_gmx_tmp directory.

2. On Liquid Phase, set gro File to gmx_tmp_mdrun.gro in c6h6_liquid_gmx_tmp directory.

3. On Vapor Phase, set edr File to gmx_tmp_mdrun.edr in c6h6_vapor_gmx_tmp directory.



The window will display Hildebrand Solubility parameter δ of Molecule A

(benzene) and DPD parameterAii between Molecule A itself.

When comparing a value to the reference value, please pay attention to units.


DPD parameter

of identical particles

Solubility parameter


To calculate χ and DPD parameter Aij, Click Select... of each file on Molecule B tab.

1. On Liquid Phase, set edr File to gmx_tmp_mdrun.edr in h2o_liquid_gmx_tmp directory.

2. On Liquid Phase, set gro File to gmx_tmp_mdrun.gro in h2o_liquid_gmx_tmp directory.

3. On Vapor Phase, set edr File to gmx_tmp_mdrun.edr in h2o_vapor_gmx_tmp directory.


Solubility parameter

DPD parameter

of identical particles


On Chi/Aij tab, χ parameter and DPD parameter (Aij-Aii ) will be displayed


Χ parameter

DPD parameter

of other particles


*Please skip this page if you do not need to execute DPD calculation.

*Please also see Winmostar LAMMPS tutorial DPD about details for DPD.

1. Click MD | DPD | DPD Cell Builder.

2. Set Density to the value of Density for DPD in P.28



1. Click MD | DPD | DPD Potential editor.

2. In the Nonbond tab, set Aij of A-A or B-B to DPD parameter Aii of identical particles

obtained in P.26. User must apply a value from either component 1 or component 2.

3. Set Aij of A-B by adding the values DPD parameter Aii and DPD parameter of Aij-Aii

obtained in P.28.

The reference of the DPD parameter between water - benzene :

A. Maiti and S. McGrother, J. Chem. Phys., 120 (3), 2014, 1594.


In this example, the value of H2O

(rounded up to the nearest integer)

was applied as identical parameter.

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